Finding and characterizing the complexes of drug like molecules with quadruplex DNA: combined use of an enhanced hydroxyl radical cleavage protocol and NMR.

Structural information on the complexes of drug like molecules with quadruplex DNAs can aid the development of therapeutics and research tools that selectively target specific quadruplex DNAs. Screening can identify candidate molecules that require additional evaluation. An enhanced hydroxyl radical cleavage protocol is demonstrated that can efficiently provide structural information on the complexes of the candidate molecules with quadruplex DNA. NMR methods have been used to offer additional structural information about the complexes as well as validate the results of the hydroxyl radical approach. This multi-step protocol has been demonstrated on complexes of the chair type quadruplex formed by the thrombin binding aptamer, d(GGTTGGTGTGGTTGG). The hydroxyl radical results indicate that NSC 176319, Cain's quinolinium that was found by screening, exhibits selective binding to the two TT loops. The NMR results are consistent with selective disruption of the hydrogen bonding between T4 and T13 as well as unstacking of these residues from the bottom quartet. Thus, the combination of screening, hydroxyl radical footprinting and NMR can find new molecules that selectively bind to quadruplex DNAs as well as provide structural information about their complexes.

In vitro structure-activity relationships of aplysinopsin analogs and their in vivo evaluation in the chick anxiety-depression model.

Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms and have been shown to possess a range of biological activities. In vitro receptor binding assays showed that of the 12 serotonin receptor subtypes, analogues showed a high affinity for the 5-HT2B and 5-HT2C receptor subtypes, with selectivity for 5-HT2B over 5-HT2C. While no conclusions could be drawn about the number and position of N-methylations, bromination at C-4 and C-5 of the indole ring resulted in greater binding affinities, with Ki's as low as 35 nM. This data, combined with previous knowledge of the CNS activity of aplysinopsin analogs, suggested that these compounds may have potential as leads for antidepressant drugs. Compounds 3c, 3u, and 3x were evaluated in the chick anxiety-depression model to assess their in vivo efficacy. Compound 3c showed a modest antidepressant effect at a dose of 30 nM/kg in the animal model.

Synthesis and evaluation of aplysinopsin analogs as inhibitors of human monoamine oxidase A and B.

Aplysinopsins are tryptophan-derived natural products that have been isolated from a variety of marine organisms. Previous studies have shown aplysinopsin analogs to possess a variety of biological activities, including modulation of neurotransmissions. A series of fifty aplysinopsin analogs was synthesized and assayed for monoamine oxidase A and B inhibitory activity. Three compounds displayed significant MAO inhibitory activity and selectivity. The compound (E)-5-[(6-bromo-1H-indol-3-yl)methylene]-2-imino-1,3-dimethylimidazolidin-4-one (3x) possessed an IC(50) of 5.6 nM at MAO-A and had a selectivity index of 80.24. An SAR study revealed that multiple N-methylations, one of which should be at position N-2', and bromination at C-5 or C-6 are important factors for MAO-A potency and selectivity.

Complexes of mismatched and complementary DNA with minor groove binders. Structures at nucleotide resolution via an improved hydroxyl radical cleavage methodology.

Tumor cell lines can replicate faster than normal cells and many also have defective DNA repair pathways. This has lead to the investigation of the inhibition of DNA repair proteins as a means of therapeutic intervention. An alternative approach is to hide or mask damaged DNA from the repair systems. We have developed a protocol to investigate the structures of the complexes of damaged DNA with drug like molecules. Nucleotide resolution structural information can be obtained using an improved hydroxyl radical cleavage protocol. The use of a dT(n) tail increases the length of the smallest fragments of interest and allows efficient co-precipitation of the fragments with poly(A). The use of a fluorescent label, on the 5' end of the dT(n) tail, in conjunction with modified cleavage reaction conditions, avoids the lifetime and other problems with (32)P labeling. The structures of duplex DNAs containing AC and CC mismatches in the presence and absence of minor groove binders have been investigated as have those of the fully complementary DNA. The results indicate that the structural perturbations of the mismatches are localized, are sequence dependent and that the presence of a mismatch can alter the binding of drug like molecules.

The influence of pomegranate by-product and punicalagins on selected groups of human intestinal microbiota.

We have examined the gut bacterial metabolism of pomegranate by-product (POMx) and major pomegranate polyphenols, punicalagins, using pH-controlled, stirred, batch culture fermentation systems reflective of the distal region of the human large intestine. Incubation of POMx or punicalagins with faecal bacteria resulted in formation of the dibenzopyranone-type urolithins. The time course profile confirmed the tetrahydroxylated urolithin D as the first product of microbial transformation, followed by compounds with decreasing number of phenolic hydroxy groups: the trihydroxy analogue urolithin C and dihydroxylated urolithin A. POMx exposure enhanced the growth of total bacteria, Bifidobacterium spp. and Lactobacillus spp., without influencing the Clostridium coccoides-Eubacterium rectale group and the C. histolyticum group. In addition, POMx increased concentrations of short chain fatty acids (SCFA) viz. acetate, propionate and butyrate in the fermentation medium. Punicalagins did not affect the growth of bacteria or production of SCFA. The results suggest that POMx oligomers, composed of gallic acid, ellagic acid and glucose units, may account for the enhanced growth of probiotic bacteria.

Colon cancer chemopreventive activities of pomegranate ellagitannins and urolithins.

Pomegranate juice derived ellagitannins and their intestinal bacterial metabolites, urolithins, inhibited TCDD-induced CYP1-mediated EROD activity in vitro with IC(50) values ranging from 56.7 microM for urolithin A to 74.8 microM for urolithin C. These compounds exhibited dose- and time-dependent decreases in cell proliferation and clonogenic efficiency of HT-29 cells. Inhibition of cell proliferation was mediated through cell cycle arrest in the G(0)/G(1) and G(2)/M stages of the cell cycle followed by induction of apoptosis. These results indicate that the ellagitannins and urolithins released in the colon upon consumption of pomegranate juice in considerable amounts could potentially curtail the risk of colon cancer development, by inhibiting cell proliferation and inducing apoptosis.

Optimization of culture conditions of Arnica montana L.: effects of mycorrhizal fungi and competing plants.

Arnica montana is a rare plant that needs special protection because of its intensive harvesting for medicinal purposes. The present work was aimed at finding optimal culture conditions for Arnica plants in order to enable their successful reintroduction into their natural stands. Plants were cultivated under controlled greenhouse conditions on substrata with different nitrogen (N) concentration. As Arnica is always colonized by arbuscular mycorrhizal fungi (AMF) in nature, a fact that has been overlooked in other similar projects, we, here, applied and tested different inocula. We found that they differed in their effectiveness, both in establishing symbiosis, assessed by the colonization parameters, and in improving the performance of Arnica, evaluated by the photosynthetic parameters derived from the fluorescence transients (JIP-test), with the inocula containing G. intraradices or composed of several Glomus strains being the most effective. The comparison was possible only on substrata with medium N, since high N did not permit the formation of mycorrhiza, while at low N, few nonmycorrhizal plants survived until the measurements and mycorrhizal plants, which were well growing, exhibited a high heterogeneity. Analysis of secondary metabolites showed clearly that mycorrhization was associated with increased concentrations of phenolic acids in roots. For some of the inocula used, a tendency for increase of the level of phenolic acids in shoots and of sesquiterpene lactones, both in roots and in shoots, was also observed. We also studied the interactions between A. montana and Dactylis glomerata, known to compete with Arnica under field conditions. When specimens from both species were cultured together, there was no effect on D. glomerata, but Arnica could retain a photosynthetic performance that permitted survivability only in the presence of AMF; without AMF, the photosynthetic performance was lower, and the plants were eventually totally outcompeted.

Effects of pomegranate chemical constituents/intestinal microbial metabolites on CYP1B1 in 22Rv1 prostate cancer cells.

The cytochrome P450 enzyme, CYP1B1, is an established target in prostate cancer chemoprevention. Compounds inhibiting CYP1B1 activity are contemplated to exert beneficial effects at three stages of prostate cancer development, that is, initiation, progression, and development of drug resistance. Pomegranate ellagitannins/microbial metabolites were examined for their CYP1B1 inhibitory activity in a recombinant CYP1B1-mediated ethoxyresorufin-O-deethylase (EROD) assay. Urolithin A, a microbial metabolite, was the most potent uncompetitive inhibitor of CYP1B1-mediated EROD activity, exhibiting 2-fold selectivity over CYP1A1, while urolithin B was a noncompetitive inhibitor with 3-fold selectivity. The punicalins and punicalagins exhibited potent CYP1A1 inhibition with 5-10-fold selectivity over CYP1B1. Urolithins, punicalins, and punicalagins were tested for their 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced CYP1 inhibitory activity in the 22Rv1 prostate cancer cell line. Urolithins A and B showed a decrease in their CYP1-mediated EROD inhibitory IC50 values upon increasing their treatment times from 30 min to 24 h. Urolithin C, 8-O-methylurolithin A, and 8,9-di-O-methylurolithin C caused a potent CYP1-mediated EROD inhibition in 22Rv1 cells upon 24 h of incubation. Neutral red uptake assay results indicated that urolithin C, 8-O-methylurolithin A, and 8,9-di-O-methylurolithin C induced profound cytotoxicity in the proximity of their CYP1 inhibitory IC50 values. Urolithins A and B were studied for their cellular uptake and inhibition of TCDD-induced CYP1B1 expression. Cellular uptake experiments demonstrated a 5-fold increase in urolithin uptake by 22Rv1 cells. Western blots of the CYP1B1 protein indicated that the urolithins interfered with the expression of CYP1B1 protein. Thus, urolithins were found to display a dual mode mechanism by decreasing CYP1B1 activity and expression.

Urolithins, intestinal microbial metabolites of Pomegranate ellagitannins, exhibit potent antioxidant activity in a cell-based assay.

Many health benefits of pomegranate products have been attributed to the potent antioxidant action of their tannin components, mainly punicalagins and ellagic acid. While moving through the intestines, ellagitannins are metabolized by gut bacteria into urolithins that readily enter systemic circulation. In this study, the antioxidant properties of seven urolithin derivatives were evaluated in a cell-based assay. This method is biologically more relevant because it reflects bioavailability of the test compound to the cells, and the antioxidant action is determined in the cellular environment. Our results showed that the antioxidant activity of urolithins was correlated with the number of hydroxy groups as well as the lipophilicity of the molecule. The most potent antioxidants are urolithins C and D with IC(50) values of 0.16 and 0.33 microM, respectively, when compared to IC(50) values of 1.1 and 1.4 microM of the parent ellagic acid and punicalagins, respectively. The dihydroxylated urolithin A showed weaker antioxidant activity, with an IC(50) value 13.6 microM, however, the potency was within the range of urolithin A plasma concentrations. Therefore, products of the intestinal microbial transformation of pomegranate ellagitannins may account for systemic antioxidant effects.

The effect of pomegranate (Punica granatum L.) byproducts and ellagitannins on the growth of human gut bacteria.

The consumption of pomegranate products leads to a significant accumulation of ellagitannins in the large intestines, where they interact with complex gut microflora. This study investigated the effect of pomegranate tannin constituents on the growth of various species of human gut bacteria. Our results showed that pomegranate byproducts and punicalagins inhibited the growth of pathogenic clostridia and Staphyloccocus aureus. Probiotic lactobacilli and bifidobacteria were generally not affected by ellagitannins, while relatively small growth inhibition by ellagic acid likely resulted from decreasing media quality due to the formation of tannin-protein complexes. The effect of pomegranate ellagitannins on bifidobacteria was species- and tannin-dependent. The growth of Bifidobacterium animalis ssp. lactis was slightly inhibited by punicalagins, punicalins, and ellagic acid. POMx supplementation significantly enhanced the growth of Bifidobacterium breve and Bifidobacterium infantis.

Aplysinopsins--marine indole alkaloids: chemistry, bioactivity and ecological significance.

Aplysinopsins are tryptophan-derived marine natural products isolated from numerous genera of sponges and scleractinian corals, as well as from one sea anemone and one nudibranch. Aplysinopsins are widely distributed in the Pacific, Indonesia, Caribbean, and Mediterranean regions. Up to date, around 30 analogues occurring in Nature have been reported. Natural aplysinopsins differ in the bromination pattern of the indole ring, variation in the structure of the C ring, including the number and position of N-methylation, the presence and configuration of the C-8-C-1' double bond, and the oxidation state of the 2-aminoimidazoline fragment. Aplysinopsins can also occur in the form of dimers. This review summarizes 30 years' research on aplysinopsins. The origin, isolation sources, chemistry, bioactivity, and ecological functions of aplysinopsins are comprehensively reviewed.

The long-term effect of cadmium exposure through food on the postnatal development of the bank vole (Clethrionomys glareolus Schreber, 1780).

Cadmium is well known for its toxicity to the animal body. However, its effect on pregnancy and the development of young animals is still not well understood. This study examined such effects, using bank voles captured from the wild to make the results closer to those which could be expected in the natural environment. One group of animals was fed 7 microg g(-1) cadmium in the food, a second 35 microg g(-1), and a third no cadmium, as a control. The concentrations of cadmium in the whole bodies of young bank voles were determined on the 3rd, 5th, or 10th day of life. The cadmium level in the bodies of animals exposed to 35 microg g(-1) of cadmium was significantly higher than in those from either the control group or the group receiving 7 microg g(-1) of cadmium, which did not differ from each other. The cadmium level did not change with animal age in any of the study groups. Concentrations of Zn, Cu, and Fe were also determined in the whole body of young animals, as cadmium is known to disturb the metabolism of these essential metals through antagonistic activity. Both Cu and Fe levels were negatively correlated with cadmium concentrations, while a positive correlation was found between zinc and cadmium in the young animal bodies. Also found was higher offspring mortality in the group receiving 35 microg g(-1) of cadmium in food. There was no difference in young animal body weight between the study groups.